Attempts are being made to introduce a next-generation sequencer to transcriptome and proteome analysis, to obtain a large amount of information on intermolecular interactions of protein/DNA/RNA (Non-patent Document 1).
A method wherein mRNA-protein assignment molecules prepared by linking mRNAs to the proteins encoded thereby via a covalent bond are used (FIG. 1, panels a and b) to obtain the amino acid sequence information of the protein as the nucleotide sequence information of DNA is known as the in vitro virus (IVV) method (Patent Document 1 and Patent Document 2). By using the IVV method and a Sanger-type DNA sequencer, proteome analysis has been carried out (Non-patent Document 2, Non-patent Document 3 and Non-patent Document 4). However, conventional methods need immobilization of a target protein (called a “bait”) on a resin for performing affinity selection (FIG. 1, panel c-1), followed by amplification of DNA by RT-PCR from mRNA linked to a protein bound to the bait (FIG. 1, panel d-1). Therefore, large-scale analysis has been in need of preparation of a large amount of baits which are to be individually subjected to affinity selection.
For example, in cases where interactions of 50 types of bait proteins were to be analyzed, it has been necessary to individually prepare the 50 types of proteins and immobilize these on a resin, followed by performing affinity selection. Such an operation is laborious and costly. Further, even if only about 50 types of bait proteins were used, the number of the obtained interactions cannot be said to be comprehensive.